Having made his debut appearance in the Season 1 episode, Sub Rosa (episode), Sean Murray and his character Timothy McGee both proved to be popular with both the actor and his character making constant appearances in various episodes of Season 1.

With McGee becoming a junior field agent under Gibbs's supervision in the Season 1 finale episode, Reveille (episode), Murray was promoted to series regular and also added to the opening credits, making his first ever debut appearance in the opening credits in the Season 2 premiere episode, See No Evil (episode).

In addition to Murray joining the series permanently, the show later introduced the Foof, numerous black and white previews which are seen at the beginning and ending of all four acts of the episode with the Foofs themselves usually lasting for three seconds. This began in the Season 2 episode, Lt. Jane Doe (episode) and has continued to this day.

The Season 2 finale episode, Twilight (episode) ended with the shocking scene of Kate Todd being shot dead at the hands of rogue Mossad and double agent, Ari Haswari, ending the episode in a cliffhanger.

Kate's death was brought on by the fact that Sasha Alexander had expressed a desire to leave the NCIS series for good after the second season in order to start a family of her own and pursue projects. Her reason for doing so as revealed by Donald P. Bellisario on the DVD release for season two, was the renewal of the series for a third season which had come as a surprise to her because no prior series with which she had been involved had lasted more than two seasons before being cancelled and as such, she had not planned to stay more than two seasons.

A Navy Captain's wife and blind daughter are kidnapped and held hostage, forcing NCIS to tackle the case of bringing both of the hostages home safely while also trying to find out who is responsible. This is the Season 2 premiere episode.

The body of a Navy Lieutenant is discovered but things hit a snag when the NCIS team learn that she is not actually a Commander while the nature of the case causes Ducky begin to become distant from the team.

The NCIS team investigate the death of a Naval Commander and they soon discover that the victim was not very well liked on the USS Kennedy while NCIS Special Agent Paula Cassidy returns to help the team with the case.

The NCIS team investigate when the wife of a Marine shoots an intruder in self-defense and as the case progresses, the team find themselves heading into the world of cyber sex along with the revelation that the intruder and his "sister" are not who they appear to be.

The NCIS team investigate the alleged death of a Petty Officer and find themselves working with a team whose personalities are an exact match to their own but things take a turn when the Petty Officer is later found dead.

Ducky's past comes back to haunt him, forcing the NCIS team to step to protect him as they also seek to determine who is responsible for the various meat puzzles. This also makes the debut appearance of Ducky's mother, Victoria Mallard.

The NCIS team investigate the claim of a young woman who believes that she saw a sailor being strangled but things take a turn for the worse when the woman herself is murdered, leaving McGee devastated and the team on the hunt to capture her killer.

The NCIS team investigate when a package containing a pair of blue human eyeballs wind up in the locker of a civilian but when the Petty Officer commits suicide during the case, Tony and Kate head to Paraguay where they discover some horrifying secrets about the Officer's lecturer.

The NCIS team investigate the death of a Petty Officer who drowned after having her head held down in a public toilet and soon discover that she was pregnant, leading them to a person who also happens to be the killer.

NCIS investigate a Petty Officer who claims that she was attacked by someone in body armor. It appears to be a simple case but tragedy strikes when the Officer is found dead, having allegedly committed suicide. Ducky however soon discovers that the victim was actually murdered, sending the team on a search for her killer as they uncover a trail of romance, sex and deception at the local mental institution that the Officer was staying at before she died.

When a Petty Officer dies while serving in Iraq, the NCIS team investigate when the remains of a young girl who went missing during their high school years are discovered in a storage unit. The team face further pressure to clear the case as quick as possible upon learning that the Officer is up for a Silver Star.

NCIS faces a huge crisis when they become victims of a biological attack and one member of the NCIS team is left fighting for their life after falling victim to the deadly disease while the rest of the NCIS team must determine who is responsible.

NCIS investigate the deaths of two sailors who were mysteriously gunned down while on leave and soon find themselves facing an enemy from their past with the battle ultimately having very dramatic and life-changing consequences for the team when one member of the NCIS team is brutally murdered...

"NCIS: The Second Season continues the mind-blowing action and pulse-pounding adventures of an elite team of special agents who operate outside the military chain of command. Led by Special Agent Leroy Jethro Gibbs (Mark Harmon), a tough, highly skilled investigator who's willing to bend the rules to get the job done, this tight-knit crew prove they're willing to pay the ultimate price when they travel the globe investigating everything from murder and espionage to terrorism and kidnapping. This 6-disc set features all 23 thrilling episodes from this unique and dynamic show".